Template repository for an analysis

Contents of the dummy package:

• template_analysis: is the directory supposed to contain all your code belonging to the repository, rename template_analysis to your desired package name
• requirements.txt: a file with external python packages used in your code
• setup.py is needed to install the current directory as a package. Edit and replace template_analysis with your package name, version number and contact details

Suggested directories in package (template_analysis)

The pre-existing directory strucure is there to help and suggest some sort of structure in your analysis. Feel free to extend and modify as needed.

• data: containing tabulated results from scripts.
• plots: containing final result plots.
• config.py: pointing to these directories and providing path variables that can be used inside scripts. May simplify repointing to different local directories if desired.

Edit plots/.gitignore and data/.gitignore or add a general .gitignore to not push huge files to github

!TODO: do we want to add a default matplotlib style?

1. Installation

Clone repository, change to the directory and install. The -e option installs the package in editable mode under the current path, which allows to edit scripts without reinstalling.

git clone git@github.com:RNO-G/template-analysis.git && cd template-analysis
pip install -r requirements.txt -e .

2. Use of template_analysis outside the package

After installing you can use all the code inside template_analysis from anywhere on your machine. You might want to use that e.g. inside jupyter notebooks...

E.g.:

(pyvenv) shallmann@Steffens-MBP ~ % python -i
Python 3.10.9 (main, Dec 15 2022, 18:25:35) [Clang 14.0.0 (clang-1400.0.29.202)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from template_analysis import example
>>> example.example()
I am a minimal example doing nothing!

3. Adding command line scripts

It is possible to add command line entry points to setup.py. As an example, run-template-analysis is set to execute the main function in template_analysis/run.py.

E.g.:

(pyvenv) shallmann@Steffens-MBP ~ % run-template-analysis -h  
usage: run-template-analysis [-h] n_points

Template analysis

positional arguments:
  n_points

options:
  -h, --help  show this help message and exit

Run with 1000 data points

(pyvenv) shallmann@Steffens-MBP ~ % run-template-analysis 1000
writing output to /Users/shallmann/Desktop/analysis-template-repo/template_analysis/data/step1_result_1000.txt
writing plot generated from /Users/shallmann/Desktop/analysis-template-repo/template_analysis/data/step1_result_1000.txt to /Users/shallmann/Desktop/analysis-template-repo/template_analysis/plots/step1_result_1000.png